Sounds as if you need to re-configure the BitSetter since the belt stretch calibration changed that position:
https://my.carbide3d.com/docs/shapeoko-setup/
Other things to check:
- all wiring in good condition and all connectors secure
- pulley set screws securely in place — put a witness mark across the end of the motor shaft/pulleys to keep an eye on whether or no the pulley shifts on the shaft
- belt tension: Measuring belt tension, squaring and calibration
- mechanical interference — make sure that nothing gets in the way of the machine moving
- lubrication — CNC Machine Maintenance